/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2020 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
 * as published by the Free Software Foundation; either version 2
 * of the License, or (at your option) any later version.
 *
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 * GNU General Public License for more details.
 *
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#ifndef _U2_MSA_CONSENSUS_ALGORITHM_DEFAULT_H_
#define _U2_MSA_CONSENSUS_ALGORITHM_DEFAULT_H_

#include "BuiltInConsensusAlgorithms.h"
#include "MSAConsensusAlgorithm.h"

namespace U2 {

// Default algorithm is based on JalView experience. It also makes letters with low threshold lowercase
class U2ALGORITHM_EXPORT MSAConsensusAlgorithmFactoryDefault : public MSAConsensusAlgorithmFactory {
    Q_OBJECT
public:
    MSAConsensusAlgorithmFactoryDefault(QObject *p = NULL);

    virtual MSAConsensusAlgorithm *createAlgorithm(const MultipleAlignment &ma, bool ignoreTrailingLeadingGaps, QObject *parent);

    virtual QString getDescription() const;

    virtual QString getName() const;

    virtual int getMinThreshold() const {
        return 1;
    }

    virtual int getMaxThreshold() const {
        return 100;
    }

    virtual int getDefaultThreshold() const {
        return 100;
    }

    virtual QString getThresholdSuffix() const {
        return QString("%");
    }

    virtual bool isSequenceLikeResult() const {
        return false;
    }
};

class U2ALGORITHM_EXPORT MSAConsensusAlgorithmDefault : public MSAConsensusAlgorithm {
    Q_OBJECT
public:
    MSAConsensusAlgorithmDefault(MSAConsensusAlgorithmFactoryDefault *f, bool ignoreTrailingLeadingGaps, QObject *p = NULL)
        : MSAConsensusAlgorithm(f, ignoreTrailingLeadingGaps, p) {
    }

    virtual char getConsensusChar(const MultipleAlignment &ma, int column, QVector<int> seqIdx = QVector<int>()) const {
        int countStub = 0;
        return getConsensusCharAndScore(ma, column, countStub, seqIdx);
    }

    virtual MSAConsensusAlgorithmDefault *clone() const;

    virtual char getConsensusCharAndScore(const MultipleAlignment &ma, int column, int &score, QVector<int> seqIdx = QVector<int>()) const;
};

}    // namespace U2

#endif
